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comparison tools/clinod/clinod.xml @ 5:9485cdfca57e draft

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v0.0.8 internal changes
author peterjc
date Wed, 05 Aug 2015 10:58:54 -0400
parents 4d9a4a43861b
children 77cfe958b5ea
comparison
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4:4d9a4a43861b 5:9485cdfca57e
1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7"> 1 <tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.8">
2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> 2 <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">java</requirement> 4 <requirement type="binary">java</requirement>
5 <requirement type="package" version="1.3">clinod</requirement> 5 <requirement type="package" version="1.3">clinod</requirement>
6 </requirements> 6 </requirements>
7 <stdio>
8 <!-- Assume anything other than zero is an error -->
9 <exit_code range="1:" />
10 <exit_code range=":-1" />
11 </stdio>
7 <command> 12 <command>
8 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder 13 ##The Galaxy Tool Shed installation should define $CLINOD to point at folder
9 ##containing both clinod-1.3.jar and the batchman binary: 14 ##containing both clinod-1.3.jar and the batchman binary:
10 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence 15 java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
11 ##TODO - Make the -clean_sequence argument a parameter? 16 ##TODO - Make the -clean_sequence argument a parameter?
12 </command> 17 </command>
13 <stdio>
14 <!-- Assume anything other than zero is an error -->
15 <exit_code range="1:" />
16 <exit_code range=":-1" />
17 </stdio>
18 <inputs> 18 <inputs>
19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
20 </inputs> 20 </inputs>
21 <outputs> 21 <outputs>
22 <data name="tabular_file" format="tabular" label="NoD results" /> 22 <data name="tabular_file" format="tabular" label="NoD results" />